HOMOLOG: Two molecules are said to homologous if they have been derived from a common ancestor. Homologous molecules or homologs are divided into two classes: paralog and ortholog. Homology is often manifested by significant similarity in nucleotide or amino acid sequence and almost always manifested in three-dimensional structure.

PARALOG: Paralogs are homologs that are present within one species. Paralogs often differ in their detailed biochemical functions. For example, human ribonuclease, which is a digestive enzyme and angiogenin, which stimulates blood vessel growth are structurally very similar but functionally very different.

ORTHOLOG: Orthologs are homologs that are present within different species and have very similar or identical functions. For example, human ribonuclease, which is a digestive enzyme and bovine ribonuclease, which is also a digestive enzyme, are both structurally similar and functionally similar but are present in different species.

SEQUENCE ALIGNMENT: Sequence alignment is a method to examine the similarity between two amino acid sequences. This method compares all possible juxtapositions of one protein structure with another and in each case recording the number of identical residues that are aligned with one another. This comparison is made by sliding one sequence past the other sequence, one amino acid at a time, and counting the number of matched residues (different scoring methods instead of identity can be used).

CONSERVATIVE SUBSTITUTION: A conservative substitution replaces one amino acid with another that is similar in size and chemical properties. Such conservative amino acid substitutions may have minor effects on protein structure and can thus be tolerated without compromising function. This leads to a need to find a better way to score the similarity of sequences.

IDENTITY MATRIX: This type of matrix scores a value of 1 for every time two amino acids or DNA base pairs align, and zero at all other times. Conservation is not taken into account.

SUBSTITUTION MATRIX: A substitution matrix is a large scoring guide to tell you how to rank the similarity of two amino acid sequences. A large positive score corresponds to a substitution that occurs frequently. A large negative score corresponds to a substitution that occurs rarely.

DIVERGENT EVOLUTION: In divergent evolution two similar aspects of an organism or the organisms themselves arise from a common ancestor or origin.

CONVERGENT EVOLUTION: In convergent evolution two proteins for example that evolved independently may have converged on a similar structure to perform a similar biochemical activity. The structure for example may have been an effective solution to a biochemical problem that both species faced. The process of different evolutionary pathways that lead to the same solution is convergent evolution. For example, both birds and insects have wings but they do not share a common ancestor.

EVOLUTIONARY TREES: Evolutionary trees are descriptive pictures in the form of a branching tree to show divergence and inheritance from a common ancestor.

COMBINATORIAL CHEMISTRY: Combinatorial chemistry is the process of producing large populations of molecules en masse and selecting between them for a particular biochemical property. First you generate a diverse population, second you select members based on a certain criterion, and third reproduce the selected members to enrich the population for even better members of the population that will fulfill the criterion even better. This method is evolution in vitro or in a laboratory, and typically utilizes PCR and affinity chromatography, which is incredibly useful for better understanding molecular evolution.